Pseudomonas putida CBB5 NdmA with theophylline

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report

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Structural and Mechanistic Insights into Caffeine Degradation by the Bacterial N-Demethylase Complex.

Kim, J.H.Kim, B.H.Brooks, S.Kang, S.Y.Summers, R.M.Song, H.K.

(2019) J Mol Biol 431: 3647-3661

  • DOI: https://doi.org/10.1016/j.jmb.2019.08.004
  • Primary Citation of Related Structures:  
    6ICK, 6ICL, 6ICM, 6ICN, 6ICO, 6ICP, 6ICQ

  • PubMed Abstract: 

    Caffeine, found in many foods, beverages, and pharmaceuticals, is the most used chemical compound for mental alertness. It is originally a natural product of plants and exists widely in environmental soil. Some bacteria, such as Pseudomonas putida CBB5, utilize caffeine as a sole carbon and nitrogen source by degrading it through sequential N-demethylation catalyzed by five enzymes (NdmA, NdmB, NdmC, NdmD, and NdmE). The environmentally friendly enzymatic reaction products, methylxanthines, are high-value biochemicals that are used in the pharmaceutical and cosmetic industries. However, the structures and biochemical properties of bacterial N-demethylases remain largely unknown. Here, we report the structures of NdmA and NdmB, the initial N 1 - and N 3 -specific demethylases, respectively. Reverse-oriented substrate bindings were observed in the substrate-complexed structures, offering methyl position specificity for proper N-demethylation. For efficient sequential degradation of caffeine, these enzymes form a unique heterocomplex with 3:3 stoichiometry, which was confirmed by enzymatic assays, fluorescent labeling, and small-angle x-ray scattering. The binary structure of NdmA with the ferredoxin domain of NdmD, which is the first structural information for the plant-type ferredoxin domain in a complex state, was also determined to better understand electron transport during N-demethylation. These findings broaden our understanding of the caffeine degradation mechanism by bacterial enzymes and will enable their use for industrial applications.

  • Organizational Affiliation

    Department of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea. Electronic address: hksong@korea.ac.kr.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methylxanthine N1-demethylase NdmA
A, B, C
369Pseudomonas putidaMutation(s): 0 
Gene Names: ndmA
Find proteins for H9N289 (Pseudomonas putida)
Explore H9N289 
Go to UniProtKB:  H9N289
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH9N289
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on TEP

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C]
C7 H8 N4 O2
Query on FES

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B],
J [auth C]
Fe2 S2
Query on CO

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.85 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.881α = 90
b = 135.881β = 90
c = 155.61γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic Of2016R1E1A1A01942623

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-04
    Type: Initial release
  • Version 1.1: 2019-09-25
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-20
    Changes: Derived calculations